3-52353165-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_015512.5(DNAH1):c.3090G>T(p.Ala1030=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A1030A) has been classified as Likely benign.
Frequency
Consequence
NM_015512.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.3090G>T | p.Ala1030= | synonymous_variant | 19/78 | ENST00000420323.7 | |
DNAH1 | XM_017006129.2 | c.3090G>T | p.Ala1030= | synonymous_variant | 20/80 | ||
DNAH1 | XM_017006130.2 | c.3090G>T | p.Ala1030= | synonymous_variant | 20/79 | ||
DNAH1 | XM_017006131.2 | c.3090G>T | p.Ala1030= | synonymous_variant | 20/79 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.3090G>T | p.Ala1030= | synonymous_variant | 19/78 | 1 | NM_015512.5 | P1 | |
DNAH1 | ENST00000486752.5 | n.3351G>T | non_coding_transcript_exon_variant | 19/77 | 2 | ||||
DNAH1 | ENST00000497875.1 | n.3255G>T | non_coding_transcript_exon_variant | 20/21 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461670Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727120
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at